Wow, this is great. Managed to use up a few hours of mine. Awesome stuff with the random maps being generated every time a new game is started.
Anyhow, I played through four times and I only picked up on a few problems so far.
Map60 (Settlement) - I was unable to open the blue door which lowers the gate to the settlement. I ended up having to no-clip inside to get past. Also, upon nearing the end of the entire mission (I was up to destroying the ATST lab I believe) I went back to the settlement area (MAP60) since I didn't write down the number of the map. Upon arriving there a generic (Doom 2) Nazi soldier waltzing around the settlement, obviously hostile. Dunno what caused that.
Map54 (Ice Slopes (I think that's the name)) - The ice patch at the south western side of the map (in the raised area) is not acting like ice, as in it still has friction unlike the rest of the icy patches in the area.
And that's it for bugs/nitpicks that I found.
I should also say that any scenarios that have the Imperial Armoury included usually are very easy to win, due to all the ammunition you get from them.
I'm going to play through it a few more times later on to complete the other missions I haven't done yet.